Just a simple bug fix. When supplying a prefix to SAMTOOLS_REHEADER, this was not being used to evaluate if input/output files were the same to trigger the error message.
PR checklist
Closes #XXX
[ ] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - have you followed the module conventions in the contribution docs
[ ] If necessary, include test data in your PR.
[ ] Remove all TODO statements.
[ ] Emit the versions.yml file.
[ ] Follow the naming conventions.
[ ] Follow the parameters requirements.
[ ] Follow the input/output options guidelines.
[ ] Add a resource label
[ ] Use BioConda and BioContainers if possible to fulfil software requirements.
Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
For modules:
[ ] nf-core modules test <MODULE> --profile docker
[ ] nf-core modules test <MODULE> --profile singularity
[ ] nf-core modules test <MODULE> --profile conda
For subworkflows:
[ ] nf-core subworkflows test <SUBWORKFLOW> --profile docker
[ ] nf-core subworkflows test <SUBWORKFLOW> --profile singularity
[ ] nf-core subworkflows test <SUBWORKFLOW> --profile conda
Just a simple bug fix. When supplying a prefix to SAMTOOLS_REHEADER, this was not being used to evaluate if input/output files were the same to trigger the error message.
PR checklist
Closes #XXX
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda